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‎Data_managment.png‎

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‎Figure_1.png‎

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‎GGD-CLI.html‎

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@@ -107,76 +107,50 @@ <h3 id="searchlabel">Quick search</h3>
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<p>The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
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description of each tool, as well as links to specific pages about each.</p>
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<p>Tabs for each tool are also available on the left tab bar.</p>
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<ol class="arabic">
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<li><p><a class="reference internal" href="ggd-search.html#ggd-search"><span class="std std-ref">ggd search</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Search for a ggd data package</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="predict-path.html#ggd-predict-path"><span class="std std-ref">ggd predict-path</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Predict the file path of a data package that has not been installed yet (Good for workflows like Snakemake)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="install.html#ggd-install"><span class="std std-ref">ggd install</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Install ggd data package(s)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="uninstall.html#ggd-uninstall"><span class="std std-ref">ggd uninstall</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Uninstall a ggd data package(s)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="list.html#ggd-list"><span class="std std-ref">ggd list</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>List the installed data packages (in a specific environment)</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="list-file.html#ggd-get-files"><span class="std std-ref">ggd get-files</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>get the files for an installed ggd package</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="pkg-info.html#ggd-pkg-info"><span class="std std-ref">ggd pkg-info</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Show a specific ggd package’s info</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="show-env.html#ggd-show-env"><span class="std std-ref">ggd show-env</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Show the ggd specific environment variables</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="make-recipe.html#ggd-make-recipe"><span class="std std-ref">ggd make-recipe</span></a></p>
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<blockquote>
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<div><ul class="simple">
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<li><p>Create a ggd recipe from a bash script</p></li>
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</ul>
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</div></blockquote>
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</li>
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<li><p><a class="reference internal" href="check-recipe.html#ggd-check-recipe"><span class="std std-ref">ggd check-recipe</span></a></p>
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<ul class="simple">
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<li><p>Check/test a ggd recipe</p></li>
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</ul>
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</li>
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</ol>
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<table class="docutils align-default">
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<colgroup>
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<col style="width: 42%" />
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<col style="width: 58%" />
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</colgroup>
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<thead>
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<tr class="row-odd"><th class="head"><p>Command</p></th>
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<th class="head"><p>Description</p></th>
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</tr>
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</thead>
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<tbody>
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<tr class="row-even"><td><p><a class="reference internal" href="ggd-search.html#ggd-search"><span class="std std-ref">ggd search</span></a></p></td>
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<td><p>Search for a ggd data package</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="predict-path.html#ggd-predict-path"><span class="std std-ref">ggd predict-path</span></a></p></td>
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<td><p>Predict the file path of a data package that has not been
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installed yet (Good for workflows like Snakemake)</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="install.html#ggd-install"><span class="std std-ref">ggd install</span></a></p></td>
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<td><p>Install ggd data package(s)</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="uninstall.html#ggd-uninstall"><span class="std std-ref">ggd uninstall</span></a></p></td>
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<td><p>Uninstall a ggd data package(s)</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="list.html#ggd-list"><span class="std std-ref">ggd list</span></a></p></td>
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<td><p>List the installed data packages (in a specific environment)</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="list-file.html#ggd-get-files"><span class="std std-ref">ggd get-files</span></a></p></td>
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<td><p>get the files for an installed ggd package</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="pkg-info.html#ggd-pkg-info"><span class="std std-ref">ggd pkg-info</span></a></p></td>
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<td><p>Show a specific ggd package’s info</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="show-env.html#ggd-show-env"><span class="std std-ref">ggd show-env</span></a></p></td>
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<td><p>Show the ggd specific environment variables</p></td>
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</tr>
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<tr class="row-even"><td><p><a class="reference internal" href="make-recipe.html#ggd-make-recipe"><span class="std std-ref">ggd make-recipe</span></a></p></td>
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<td><p>Create a ggd recipe from a bash script</p></td>
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</tr>
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<tr class="row-odd"><td><p><a class="reference internal" href="check-recipe.html#ggd-check-recipe"><span class="std std-ref">ggd check-recipe</span></a></p></td>
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<td><p>Check/test a ggd recipe</p></td>
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</tr>
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</tbody>
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</table>
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<p>Command links:</p>
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<div class="toctree-wrapper compound">
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<ul>

‎GGD-CLI.rst‎

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.. _ggd_cli_page:
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GGD Commands
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============
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[:ref:`Click here to return to the home page <home-page>`]
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**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`
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The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
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description of each tool, as well as links to specific pages about each.
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Tabs for each tool are also available on the left tab bar.
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+-------------------------------------------------+--------------------------------------------------------------------+
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| Command | Description |
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+=================================================+====================================================================+
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| :ref:`ggd search <ggd-search>` | Search for a ggd data package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd predict-path <ggd-predict-path>` | Predict the file path of a data package that has not been |
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| | installed yet (Good for workflows like Snakemake) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd install <ggd-install>` | Install ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd uninstall <ggd-uninstall>` | Uninstall a ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd list <ggd-list>` | List the installed data packages (in a specific environment) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd get-files <ggd-get-files>` | get the files for an installed ggd package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd pkg-info <ggd-pkg-info>` | Show a specific ggd package's info |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd show-env <ggd-show-env>` | Show the ggd specific environment variables |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd make-recipe <ggd-make-recipe>` | Create a ggd recipe from a bash script |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd check-recipe <ggd-check-recipe>` | Check/test a ggd recipe |
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+-------------------------------------------------+--------------------------------------------------------------------+
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Command links:
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.. toctree::
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:maxdepth: 2
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ggd-search
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install
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predict-path
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uninstall
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list
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list-file
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pkg-info
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show-env
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make-recipe
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check-recipe

‎GGD-framework.png‎

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‎GGD_Cloud.png‎

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‎GoGetData_name_logo.png‎

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‎_sources/GGD-CLI.rst.txt‎

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Tabs for each tool are also available on the left tab bar.
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1. :ref:`ggd search <ggd-search>`
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* Search for a ggd data package
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2. :ref:`ggd predict-path <ggd-predict-path>`
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* Predict the file path of a data package that has not been installed yet (Good for workflows like Snakemake)
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3. :ref:`ggd install <ggd-install>`
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* Install ggd data package(s)
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4. :ref:`ggd uninstall <ggd-uninstall>`
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* Uninstall a ggd data package(s)
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5. :ref:`ggd list <ggd-list>`
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* List the installed data packages (in a specific environment)
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6. :ref:`ggd get-files <ggd-get-files>`
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* get the files for an installed ggd package
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7. :ref:`ggd pkg-info <ggd-pkg-info>`
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* Show a specific ggd package's info
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8. :ref:`ggd show-env <ggd-show-env>`
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* Show the ggd specific environment variables
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9. :ref:`ggd make-recipe <ggd-make-recipe>`
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* Create a ggd recipe from a bash script
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10. :ref:`ggd check-recipe <ggd-check-recipe>`
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* Check/test a ggd recipe
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+-------------------------------------------------+--------------------------------------------------------------------+
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| Command | Description |
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+=================================================+====================================================================+
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| :ref:`ggd search <ggd-search>` | Search for a ggd data package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd predict-path <ggd-predict-path>` | Predict the file path of a data package that has not been |
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| | installed yet (Good for workflows like Snakemake) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd install <ggd-install>` | Install ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd uninstall <ggd-uninstall>` | Uninstall a ggd data package(s) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd list <ggd-list>` | List the installed data packages (in a specific environment) |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd get-files <ggd-get-files>` | get the files for an installed ggd package |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd pkg-info <ggd-pkg-info>` | Show a specific ggd package's info |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd show-env <ggd-show-env>` | Show the ggd specific environment variables |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd make-recipe <ggd-make-recipe>` | Create a ggd recipe from a bash script |
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+-------------------------------------------------+--------------------------------------------------------------------+
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| :ref:`ggd check-recipe <ggd-check-recipe>` | Check/test a ggd recipe |
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+-------------------------------------------------+--------------------------------------------------------------------+
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